PMcomp / PMmulti

Structural Alignment of RNA

pmcomp and
pmmulti are two programs to perfrom pairwise and
progressive multiple alignments of RNA sequences. pmcomp is
a variant of Sankoff's algorithm for simultaneous folding and
alignment, which takes as input pre-computed base pair probability
matrices from McCaskill's algorithm as produced by RNAfold
-p. Thus the method can also be viewed as way to compare base pair
probability matrices.pmmulti is a simple wrapper program that does progressive
multiple alignments by repeatedly calling pmcomp

Program
At the moment we offer prototypes for the programs written in Perl. A
faster C version will hopefully follow soon.
Use the following links to download the pmcomp.pl (updated 11/9/04) and
pmmulti.pl
scripts.

Manual
Run pmcomp.pl --man or pmmulti.pl --man to view
the respective man pages.